tbuckley/cabot-search huggingface dataset:
Prevalence of sexually transmitted infections and bacterial vaginosis among women in sub-Saharan Africa: An individual participant data meta-analysis of 18 HIV prevention studies
Authors: Elizabeth A. Torrone, Charles S. Morrison, Pai-Lien Chen, Cynthia Kwok, Suzanna C. Francis, Richard J. Hayes, Katharine J. Looker, Sheena McCormack, Nuala McGrath, Janneke H. H. M. van de Wijgert, Deborah Watson-Jones, Nicola Low, Sami L. Gottlieb
Journal: PLoS Medicine (2018)

Background Estimates of sexually transmitted infection (STI) prevalence are essential for efforts to prevent and control STIs. Few large STI prevalence studies exist, especially for low- and middle-income countries (LMICs). Our primary objective was to estimate the prevalence of chlamydia, gonorrhea, trichomoniasis, syphilis, herpes simplex virus type 2 (HSV-2), and bacterial vaginosis (BV) among women in sub-Saharan Africa by age, region, and population type. Methods and findings We analyzed individual-level data from 18 HIV prevention studies (cohort studies and randomized controlled trials; conducted during 1993–2011), representing >37,000 women, that tested participants for ≥1 selected STIs or BV at baseline. We used a 2-stage meta-analysis to combine data. After calculating the proportion of participants with each infection and standard error by study, we used a random-effects model to obtain a summary mean prevalence of each infection and 95% confidence interval (CI) across ages, regions, and population types. Despite substantial study heterogeneity for some STIs/populations, several patterns emerged. Across the three primary region/population groups (South Africa community-based, Southern/Eastern Africa community-based, and Eastern Africa higher-risk), prevalence was higher among 15–24-year-old than 25–49-year-old women for all STIs except HSV-2. In general, higher-risk populations had greater prevalence of gonorrhea and syphilis than clinic/community-based populations. For chlamydia, prevalence among 15–24-year-olds was 10.3% (95% CI: 7.4%, 14.1%; I2 = 75.7%) among women specifically recruited from higher-risk settings for HIV in Eastern Africa and was 15.1% (95% CI: 12.7%, 17.8%; I2 = 82.3%) in South African clinic/community-based populations. Among clinic/community-based populations, prevalence was generally greater in South Africa than in Southern/Eastern Africa for most STIs; for gonorrhea, prevalence among 15–24-year-olds was 4.6% (95% CI: 3.3%, 6.4%; I2 = 82.8%) in South Africa and was 1.7% (95% CI: 1.2%, 2.6%; I2 = 55.2%) in Southern/Eastern Africa. Across the three primary region/population groups, HSV-2 and BV prevalence was high among 25–49-year-olds (ranging from 70% to 83% and 33% to 44%, respectively). The main study limitation is that the data are not from random samples of the target populations. Conclusions Combining data from 18 HIV prevention studies, our findings highlight important features of STI/BV epidemiology among sub-Saharan African women. This methodology can be used where routine STI surveillance is limited and offers a new approach to obtaining critical information on STI and BV prevalence in LMICs.
Endogenous Viral Elements in Shrew Genomes Provide Insights into <i>Pestivirus</i> Ancient History
Authors: Yiqiao Li, Magda Bletsa, Zafeiro Zisi, Ine Boonen, Sophie Gryseels, Liana Kafetzopoulou, Joanne P Webster, Stefano Catalano, Oliver G Pybus, Frederik Van de Perre, Haotian Li, Yaoyao Li, Yuchun Li, Alexei Abramov, Petros Lymberakis, Philippe Lemey, Sébastian Lequime
Journal: Molecular Biology and Evolution (2022)

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.
Evolutionary History and Strength of Selection Determine the Rate of Antibiotic Resistance Adaptation
Authors: Sandra Cisneros-Mayoral, Lucía Graña-Miraglia, Deyanira Pérez-Morales, Rafael Peña-Miller, Ayari Fuentes-Hernández
Journal: Molecular Biology and Evolution (2022)

Abstract Bacterial adaptation to stressful environments often produces evolutionary constraints whereby increases in resistance are associated with reduced fitness in a different environment. The exploitation of this resistance-cost trade-off has been proposed as the basis of rational antimicrobial treatment strategies designed to limit the evolution of drug resistance in bacterial pathogens. Recent theoretical, laboratory, and clinical studies have shown that fluctuating selection can maintain drug efficacy and even restore drug susceptibility, but can also increase the rate of adaptation and promote cross-resistance to other antibiotics. In this paper, we combine mathematical modeling, experimental evolution, and whole-genome sequencing to follow evolutionary trajectories towards β-lactam resistance under fluctuating selective conditions. Our experimental model system consists of eight populations of Escherichia coli K12 evolving in parallel to a serial dilution protocol designed to dynamically control the strength of selection for resistance. We implemented adaptive ramps with mild and strong selection, resulting in evolved populations with similar levels of resistance, but with different evolutionary dynamics and diverging genotypic profiles. We found that mutations that emerged under strong selection are unstable in the absence of selection, in contrast to resistance mutations previously selected in the mild selection regime that were stably maintained in drug-free environments and positively selected for when antibiotics were reintroduced. Altogether, our population dynamics model and the phenotypic and genomic analysis of the evolved populations show that the rate of resistance adaptation is contingent upon the strength of selection, but also on evolutionary constraints imposed by prior drug exposures.
COVID-19 mortality and excess mortality among working-age residents in California, USA, by occupational sector: a longitudinal cohort analysis of mortality surveillance data
Authors: Yea-Hung Chen, Alicia R Riley, Kate A Duchowny, Hélène E Aschmann, Ruijia Chen, Mathew V Kiang, Alyssa C Mooney, Andrew C Stokes, M Maria Glymour, Kirsten Bibbins-Domingo
Journal: The Lancet Public Health (2022)

During the first year of the COVID-19 pandemic, workers in essential sectors had higher rates of SARS-CoV-2 infection and COVID-19 mortality than those in non-essential sectors. It is unknown whether disparities in pandemic-related mortality across occupational sectors have continued to occur during the periods of SARS-CoV-2 variants and vaccine availability.
Risk factors for workplace sexual harassment and violence among a national cohort of women in Iceland: a cross-sectional study
Authors: Svava Dogg Jonsdottir, Arna Hauksdottir, Thor Aspelund, Johanna Jakobsdottir, Harpa Runarsdottir, Berglind Gudmundsdottir, Gunnar Tomasson, Unnur Anna Valdimarsdottir, Thorhildur Halldorsdottir, Edda Bjork Thordardottir
Journal: The Lancet Public Health (2022)

Sexual harassment and violence in the workplace are a serious public health concern for women worldwide with substantial costs due to sick leave and personnel turnover. Yet little is known about the prevalence of sexual harassment and violence at a population level, especially across work sectors. The aim of this study was to investigate the prevalence of workplace sexual harassment and violence by demographic factors and work sectors among Icelandic women.
Gender differences in the association between unpaid labour and mental health in employed adults: a systematic review
Authors: Jennifer Ervin, Yamna Taouk, Ludmila Fleitas Alfonzo, Belinda Hewitt, Tania King
Journal: The Lancet Public Health (2022)

Globally, billions of hours are spent on unpaid labour every year, a burden that is disproportionately carried by women. However, the potential health effects of unpaid labour have largely been unexplored. This Review examines the gendered association between unpaid labour and mental health among employed adults. We did a search of six databases and examined the association between different forms of unpaid labour and mental health. 19 studies (totalling 70 310 participants) were included. We found substantial heterogeneity, and low-to-moderate methodological quality, in the existing research. Our Review indicates substantial gender differences in exposure to unpaid labour and confirms persistent inequities in the division of unpaid work. Overall, our findings indicate that, among employed adults, unpaid labour is negatively associated with women's mental health, with effects less apparent for men. Globally, women spend a greater number of hours on unpaid labour; this review suggests that inequities in the division of unpaid labour expose women to greater risk of poorer mental health than men.
The effect of a proof-of-vaccination requirement, incentive payments, and employer-based mandates on COVID-19 vaccination rates in New York City: a synthetic-control analysis
Authors: Ezra Cohn, Michael Chimowitz, Theodore Long, Jay K Varma, Dave A Chokshi
Journal: The Lancet Public Health (2022)

COVID-19 vaccines have been available to all adults in the USA since April, 2021, but many adults remain unvaccinated. We aimed to assess the joint effect of a proof-of-vaccination requirement, incentive payments, and employer-based mandates on rates of adult vaccination in New York City (NYC).We constructed a synthetic control group for NYC composed of other counties in the core of large, metropolitan areas in the USA. The vaccination outcomes for NYC were compared against those of the synthetic control group from July 26, 2021, to Nov 1, 2021, to determine the differential effects of the policies. Analyses were conducted on county-level vaccination data reported by the Centers for Disease Control and Prevention. The synthetic control group was constructed by matching on county-level preintervention vaccination outcomes, partisanship, economic attributes, demographics, and metropolitan area population. Statistical inference was conducted using placebo tests for non-treated counties.The synthetic control group resembled NYC across attributes used in the matching process. The cumulative adult vaccination rate for NYC (in adults aged 18 years or older who received at least one dose of an authorised COVID-19 vaccine) increased from 72·5% to 89·4% (+16·9 percentage points [pp]) during the intervention period, compared with an increase from 72·5% to 83·2% (+10·7 pp) for the synthetic control group, a difference of 6·2 pp (95% CI 1·4-10·7), or 410 201 people (90 966-706 532). Daily vaccinations for NYC were consistently higher than those in the synthetic control group, a pattern that started shortly after the start of the intervention period.The combination of a proof-of-vaccination requirement, incentive payments, and vaccine mandates increased vaccination rates among adults in NYC compared with jurisdictions that did not use the same measures. Whether the impact of these measures occurred by inducing more people to get vaccinated, or by accelerating vaccinations that would have occurred later, the increase in vaccination rates likely averted illness and death.None.
Accumulation of copy number alterations and clinical progression across advanced prostate cancer
Authors: Emily Grist, Stefanie Friedrich, Christopher Brawley, Larissa Mendes, Marina Parry, Adnan Ali, Aine Haran, Alex Hoyle, Claire Gilson, Sharanpreet Lall, Leila Zakka, Carla Bautista, Alex Landless, Karolina Nowakowska, Anna Wingate, Daniel Wetterskog, A. M. Mahedi Hasan, Nafisah B. Akato, Malissa Richmond, Sofeya Ishaq, Nik Matthews, Anis A. Hamid, Christopher J. Sweeney, Matthew R. Sydes, Daniel M. Berney, Stefano Lise, Mahesh K. B. Parmar, Noel W. Clarke, Nicholas D. James, Paolo Cremaschi, Louise C. Brown, Gerhardt Attard
Journal: Genome Medicine (2022)

Genomic copy number alterations commonly occur in prostate cancer and are one measure of genomic instability. The clinical implication of copy number change in advanced prostate cancer, which defines a wide spectrum of disease from high-risk localised to metastatic, is unknown.
Epinephrine Dosing and Post–Cardiac Arrest Targeted Temperature Management—Injury Severity After Resuscitation
Authors: Daria Zaitseva, Benjamin S. Abella
Journal: JAMA Network Open (2022)

Betty Y. Yang, MD, MS; Natalie Bulger, MS; Richard Chocron, MD, PhD; Catherine R. Counts, PhD, MHA; Chris Drucker, PhD; Lihua Yin, MBA; Megin Parayil, MPH; Nicholas J. Johnson, MD; Nona Sotoodehenia, MD, MPH; Peter J. Kudenchuk, MD; Michael R. Sayre, MD; Thomas D. Rea, MD, MPH
The mental and physical health of young carers: a systematic review
Authors: Rebecca E Lacey, Baowen Xue, Anne McMunn
Journal: The Lancet Public Health (2022)

The health of those who care for someone with a health condition or advanced age is poorer, on average, than non-carers. However, the health of young carers (<18 years of age) has been under-researched, especially in quantitative studies. This systematic review aimed to summarise studies assessing the mental and physical health of young carers. 1162 unique studies were screened and 14 associations between being a young carer and health were identified (two studies were treated as a single unit of analysis as they had information from the same sample). Most of the included studies were done in the UK, with the remaining studies done in the USA, Canada, Australia, and Austria. A cross-European study of 21 countries was also included. Five of the included studies investigated both mental and physical health outcomes, seven studies investigated only mental health outcomes, and one study investigated only physical health outcomes of being a young carer. All of the included studies, except one, were cross-sectional in design. Most studies found that young carers had poorer physical and mental health, on average, than their non-caregiving peers. However, the evidence is relatively weak and more quantitative research is needed, particularly research that is longitudinal in design and assesses physical health outcomes.
Diet and Exercise in Cancer Metabolism
Authors: Jason W. Locasale
Journal: Cancer Discovery (2022)

Summary: Diet and exercise are modifiable lifestyle factors known to have a major influence on metabolism. Clinical practice addresses diseases of altered metabolism such as diabetes or hypertension by altering these factors. Despite enormous public interest, there are limited defined diet and exercise regimens for patients with cancer. Nevertheless, the molecular basis of cancer has converged over the past 15 years on an essential role for altered metabolism in cancer. However, our understanding of the molecular mechanisms that underlie the impact of diet and exercise on cancer metabolism is in its very early stages. In this perspective, I propose conceptual frameworks for understanding the consequences of diet and exercise on cancer cell metabolism and tumor biology and also highlight recent developments. By advancing our mechanistic understanding, I will discuss actionable ways that such interventions could eventually reach the mainstay of both medical oncology and cancer control and prevention.
Overall Survival Benefits of Cancer Drugs Approved in China From 2005 to 2020
Authors: Yichen Zhang, Huseyin Naci, Anita K. Wagner, Ziyue Xu, Yu Yang, Jun Zhu, Jiafu Ji, Luwen Shi, Xiaodong Guan
Journal: JAMA Network Open (2022)

<h3>Importance</h3> Of approximately 9 million patients with cancer in China in 2020, more than half were diagnosed with late-stage cancers. Recent regulatory reforms in China have focused on improving the availability of new cancer drugs. However, evidence on the clinical benefits of new cancer therapies authorized in China is not available. <h3>Objective</h3> To characterize the clinical benefits of cancer drugs approved in China, as defined by the availability and magnitude of statistically significant overall survival (OS) results. <h3>Design, Setting, and Participants</h3> This mixed-methods study comprising a systematic review and cross-sectional analysis identified antineoplastic agents approved in China between January 1, 2005, and December 31, 2020, using publicly available data and regulatory review documents issued by the National Medical Products Administration. The literature published up to June 30, 2021, was reviewed to collect results on end points used in pivotal trials supporting cancer drug approvals. <h3>Main Outcomes and Measures</h3> The primary outcome measure was a documented statistically significant positive OS difference between a new cancer therapy and a comparator treatment. Secondary outcome measures were the magnitude of OS benefit and other primary efficacy measures in pivotal trials. <h3>Results</h3> Between 2005 and 2020, 78 cancer drugs corresponding to 141 indications were authorized in China, including 20 drugs (25.6%) (for 30 indications) approved in China only. Of all indications, 26 (18.4%) were evaluated in single-arm or dose-optimization trials, most of which were authorized after 2017. By June 30, 2021, 34 drug indications (24.1%) had a documented lack of OS gain. For 68 indications (48.2%) that had documented evidence of OS benefit, the median magnitude of OS improvement was 4.1 (range, 1.0-35.0) months. After a median follow-up of 1.9 (range, 1.0-11.1) years from approval, OS data for 13 indications (9.2%) were either not reported or were still not mature. Fewer than one-third of cancer drug indications approved in China only had documented evidence of OS benefits (9 of 30 [30.0%]), whereas more than one-half of the cancer drug indications also available in the US or Europe had OS benefits (59 of 111 [53.1%]). <h3>Conclusions and Relevance</h3> In this study, almost half of cancer drug indications approved in China had demonstrated OS gain. With the increase of cancer drug approvals based on single-arm trials or immature survival data in recent years, these findings highlight the need to routinely monitor the clinical benefits of new cancer therapies in China.
Reforming the public health system in England
Authors: David J Hunter, Peter Littlejohns, Albert Weale
Journal: The Lancet Public Health (2022)

The abolition of Public Health England (PHE) during the COVID-19 pandemic has raised concerns about the future of the public health system in the UK, particularly in England. The two new bodies established in haste to replace PHE prompt reflection on the executive agency's fate and the need to identify any lessons to ensure that a public health system is put in place that is fit for purpose. The UK COVID-19 Inquiry provides an opportunity to make recommendations, but it will need to act quickly to avoid recommendations being ignored. Two areas of concern are highlighted in this Viewpoint: the respective remits of the new bodies and their governance arrangements. Both issues demand urgent attention if the new structures are to succeed and avoid a similar fate to that which befell PHE. But underlying these concerns is a much larger challenge arising from the UK's broken political system. The political system in the UK suffers from several systemic weaknesses, including departmentalism, poor implementation, an inability or unwillingness of those in power to listen to the truth, and chronic short-termism at the expense of long-term planning. Overhauling the UK's dysfunctional political system is a prerequisite for successfully improving the public health system.
The Principles and Practice of Gynecology, for Students and Practitioners.
Journal: JAMA (1905)

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Hepatocyte-targeted delivery of imiquimod reduces hepatitis B virus surface antigen
Authors: Nojoud AL Fayez, Elham Rouhollahi, Chun Yat Ong, Jiamin Wu, Anne Nguyen, Roland Böttger, Pieter R. Cullis, Dominik Witzigmann, Shyh-Dar Li
Journal: Journal of Controlled Release (2022)